History of divergence and gene flow shaping geographic variation in Andean warblers (Myioborus)

Studying how genetic variation is structured across space, and how it relates to divergence in phenotypic traits relevant to reproductive isolation, is important for our understanding of the speciation process. We used ddRAD-seq data to examine genetic variation across the distribution of an Andean warbler species complex (Myioborus ornatus–melanocephalus), which includes a known hybrid zone between two taxa with striking plumage differences. Genetic structure reflects geographic variation in head plumage, with some breaks coinciding with major topographic barriers in the Andes. We found that M. o. chrysops and M. m. bairdi, the two hybridizing taxa, were characterized by low overall genetic divergence. Based on our cline analyses of plumage and genomic hybrid indices, this hybrid zone extends for approximately 250 km, where advanced generation hybrids are likely most common. We also identified a slight difference in the geographic centers of the plumage and genetic ancestry clines, potentially suggesting asymmetric introgression of chrysops-like plumage traits. By studying genetic variation in a phenotypically diverse group distributed across a topographically complex area that includes a hybrid zone, we show how both geographic features and plumage traits potentially relevant to mate choice may contribute to species formation and maintenance in tropical mountains.